X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fanalysis%2Fscoremodels%2FSWScoreModel.js;fp=site%2Fj2s%2Fjalview%2Fanalysis%2Fscoremodels%2FSWScoreModel.js;h=e2e0eef8b394d1b6ca4aeb499b1e9afc85cf9b48;hp=06ef966ed1cf6bfc81a16a1ce90ce2b37edfaadb;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/analysis/scoremodels/SWScoreModel.js b/site/j2s/jalview/analysis/scoremodels/SWScoreModel.js
index 06ef966..e2e0eef 100644
--- a/site/j2s/jalview/analysis/scoremodels/SWScoreModel.js
+++ b/site/j2s/jalview/analysis/scoremodels/SWScoreModel.js
@@ -1,45 +1,45 @@
-Clazz.declarePackage ("jalview.analysis.scoremodels");
-Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.SWScoreModel", ["jalview.analysis.AlignSeq", "jalview.util.Comparison"], function () {
-c$ = Clazz.declareType (jalview.analysis.scoremodels, "SWScoreModel", null, jalview.api.analysis.ScoreModelI);
-Clazz.overrideMethod (c$, "findDistances", 
-function (seqData) {
-var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray ();
-var noseqs = sequenceString.length;
-var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);
-var max = -1;
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-var as =  new jalview.analysis.AlignSeq (sequenceString[i], sequenceString[j], seqData.isNa () ? "dna" : "pep");
-as.calcScoreMatrix ();
-as.traceAlignment ();
-as.printAlignment (System.out);
-distance[i][j] = as.maxscore;
-if (max < distance[i][j]) {
-max = distance[i][j];
-}}
-}
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-distance[i][j] = max - distance[i][j];
-distance[j][i] = distance[i][j];
-}
-}
-return distance;
-}, "jalview.datamodel.AlignmentView");
-Clazz.overrideMethod (c$, "getName", 
-function () {
-return "Smith Waterman Score";
-});
-Clazz.overrideMethod (c$, "isDNA", 
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "isProtein", 
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "toString", 
-function () {
-return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
-});
-});
+Clazz.declarePackage ("jalview.analysis.scoremodels");
+Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.SWScoreModel", ["jalview.analysis.AlignSeq", "jalview.util.Comparison"], function () {
+c$ = Clazz.declareType (jalview.analysis.scoremodels, "SWScoreModel", null, jalview.api.analysis.ScoreModelI);
+Clazz.overrideMethod (c$, "findDistances", 
+function (seqData) {
+var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray ();
+var noseqs = sequenceString.length;
+var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);
+var max = -1;
+for (var i = 0; i < (noseqs - 1); i++) {
+for (var j = i; j < noseqs; j++) {
+var as =  new jalview.analysis.AlignSeq (sequenceString[i], sequenceString[j], seqData.isNa () ? "dna" : "pep");
+as.calcScoreMatrix ();
+as.traceAlignment ();
+as.printAlignment (System.out);
+distance[i][j] = as.maxscore;
+if (max < distance[i][j]) {
+max = distance[i][j];
+}}
+}
+for (var i = 0; i < (noseqs - 1); i++) {
+for (var j = i; j < noseqs; j++) {
+distance[i][j] = max - distance[i][j];
+distance[j][i] = distance[i][j];
+}
+}
+return distance;
+}, "jalview.datamodel.AlignmentView");
+Clazz.overrideMethod (c$, "getName", 
+function () {
+return "Smith Waterman Score";
+});
+Clazz.overrideMethod (c$, "isDNA", 
+function () {
+return true;
+});
+Clazz.overrideMethod (c$, "isProtein", 
+function () {
+return true;
+});
+Clazz.overrideMethod (c$, "toString", 
+function () {
+return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+});
+});